Studying stochastic systems biology of the cell with single-cell genomics data
Recent experimental developments in genome-wide RNA quantification hold considerable
promise for systems biology. However, rigorously probing the biology of living cells requires …
promise for systems biology. However, rigorously probing the biology of living cells requires …
[HTML][HTML] Deciphering transcriptional dynamics in vivo by counting nascent RNA molecules
Deciphering how the regulatory DNA sequence of a gene dictates its expression in
response to intra and extracellular cues is one of the leading challenges in modern …
response to intra and extracellular cues is one of the leading challenges in modern …
Single-molecule approaches to stochastic gene expression
A Raj, A van Oudenaarden - Annual review of biophysics, 2009 - annualreviews.org
Both the transcription of mRNAs from genes and their subsequent translation into proteins
are inherently stochastic biochemical events, and this randomness can lead to substantial …
are inherently stochastic biochemical events, and this randomness can lead to substantial …
A single molecule view of gene expression
Analyzing the expression of single genes in single cells appears minimalistic in comparison
to gene expression studies based on more global approaches. However, stimulated by …
to gene expression studies based on more global approaches. However, stimulated by …
Integrating single-molecule experiments and discrete stochastic models to understand heterogeneous gene transcription dynamics
The production and degradation of RNA transcripts is inherently subject to biological noise
that arises from small gene copy numbers in individual cells. As a result, cellular RNA levels …
that arises from small gene copy numbers in individual cells. As a result, cellular RNA levels …
[HTML][HTML] The chemical fluctuation theorem governing gene expression
Gene expression is a complex stochastic process composed of numerous enzymatic
reactions with rates coupled to hidden cell-state variables. Despite advances in single-cell …
reactions with rates coupled to hidden cell-state variables. Despite advances in single-cell …
[HTML][HTML] Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments
The question of how cell-to-cell differences in transcription rate affect RNA count
distributions is fundamental for understanding biological processes underlying transcription …
distributions is fundamental for understanding biological processes underlying transcription …
[PDF][PDF] Monod: mechanistic analysis of single-cell RNA sequencing count data
We present the Python package Monod for the analysis of single-cell RNA sequencing count
data through chemical master equation models. Monod can effectively identify biological …
data through chemical master equation models. Monod can effectively identify biological …
The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations
G Lillacci, M Khammash - Bioinformatics, 2013 - academic.oup.com
Motivation: In the noisy cellular environment, stochastic fluctuations at the molecular level
manifest as cell–cell variability at the population level that is quantifiable using high …
manifest as cell–cell variability at the population level that is quantifiable using high …
[HTML][HTML] Simulating multiple faceted variability in single cell RNA sequencing
The abundance of new computational methods for processing and interpreting
transcriptomes at a single cell level raises the need for in silico platforms for evaluation and …
transcriptomes at a single cell level raises the need for in silico platforms for evaluation and …